[chimerax-users] ChimeraX: chashes in no-gui execution

Enrico Martinez jmsstarlight at gmail.com
Thu Jun 16 06:09:16 PDT 2022


Dear ChimeraX users!
I noticed that sometimes ChimeraX crashes while being executed in
batch mode using bash script.

Here is an example of my script that calculates hbonds and contacts
between protein and ligand

open mypdb.pdb
#calculate h-bonds and contacts in each frame
hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false
interModel false makePseudobonds false log true distSlop 0.5 angleSlop
20 intraRes false saveFile hbondsALL_rep1.log
clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff
0.3 interModel false makePseudobonds false log true intraRes false
saveFile contactsALL_rep1.log
wait
wait
exit

as you may see I added two times wait in the end of the script that
could reduce the frequency of crashes. May you specify what is the
default value for each wait (in seconds??) and how I could use just
one wait command to set up the pause in the proper way?
Many thanks in advance!
Cheers
Enrico


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